Analysis of Pancreatic Adenocarcinoma The Cancer Genome Atlas (TCGA) PanCancer data (Cerami et al. 2012; The Cancer Genome Atlas Research Network 2018)
Pancreatic cancers estimated deaths rank 3rd across cancers in USA in 2025 (Siegel et al. 2025) -> relevant data
Data contained cancer genomic data, scores and classification -> enough information to perform analysis
After initial analysis it didn’t look tidy -> ideal for the project purposes
Parts of image TCGA-2L-AAQI-01Z taken from (Cerami et al. 2012; The Cancer Genome Atlas Research Network 2018; David Gutman and Lee Cooper, n.d.)
Materials:
Pancreatic Adenocarcinoma The Cancer Genome Atlas (TCGA) PanCancer dataset (Cerami et al. 2012; The Cancer Genome Atlas Research Network 2018)
R studio (R, tidyverse)
draw.io (just presentation)
Methodology
PCA reduced the data to a few components while retaining most of the variance.
PCA loadings were plotted and revealed groups of strongly correlated variables, indicating redundancy in the feature set.
Genomic instability is present at all AJCC stages, not just in advanced disease.
data_gene_code_filtered |>
left_join(stage_labels, by = "NDSA_stage") |>
pivot_longer(
cols = c(
`Fraction Genome Altered`,
`Mutation Count`,
`Tumor Break Load`
),
names_to = "Genomic_Metric",
values_to = "Value"
) |>
ggplot(aes(x = stage_label, y = Value)) +
geom_violin() +
geom_boxplot(width = 0.2) +
facet_wrap(~ Genomic_Metric,
scales = "free_y",
ncol = 1) +
theme_uniform() +
theme(axis.text.x = element_text(angle = 45,
hjust = 1)) +
labs(
x = "AJCC stage (n per stage)",
y = "Genomic metric",
title = "Genomic instability metrics across
AJCC stages")Tumor structural instability interacts with hypoxia to influence survival, highlighting biologically aggressive tumor subtypes.
High Hypoxia and high Tumor Break Load leads to worst survival.
Mixed groups outperform ‘low/low’, suggesting that one single adverse factor can moderate the negative effect in survival.
Low oxygen levels in tumors Hypoxia are usually associated with resistance to radiation therapy.
Buffa Score: Higher hypoxia → unexpectedly better survival
Ragnum Score: Lower hypoxia → clear survival advantage
Winter Score: Lower hypoxia → better survival, but less pronounced than Ragnum
Variations in hypoxia scoring limit interpretation of radiotherapy survival.
:::::
Scoring methods poorly agree, labeling patients and tumors inconsistently.
Buffa and Winter align, but others disagree on hypoxia, MSI.
Buffa and Ragnum scores rose with grade, especially in tumors.
Results for patients outside the 50–80 age range should be interpreted cautiously due to low sample counts.
Predominantly White patient representation highlights the need for greater ethnic diversity.
Limited variability in several categories may constrain findings.
Future analyses could be strengthened by adding more clinical and molecular data and increasing sample diversity, including underrepresented groups.
R for Bio Data Science 2025 - Group 25 Project